This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.
When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
setwd('/Users/zhassulan_zhaniyazov/Desktop/trgn510/mygraph2/bin')
mygenes <- read.csv('gene_dist_head.tsv', header= TRUE, sep = "\t", fill = TRUE)
autosomes <- c("1","2","3","4","5","6","7","8","9","10",
"11","12","13","14","15","16","17","18","19","20","21","22")
genes <- mygenes[which(mygenes$chr %in% autosomes),]
genes$chr <- factor(genes$chr, levels = autosomes)
You can also embed plots, for example:
library(ggplot2)
ggplot(data = genes) +
geom_bar(mapping = aes(x = chr, fill = feature), width = 1) +
coord_polar()
library(plotly)
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
p <- ggplot(data = genes) +
geom_bar(mapping = aes(x = chr, fill = feature), width = 1)
ggplotly(p)
Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.